Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 290 of 290
Found at i:100220835 original size:29 final size:29
Alignment explanation
Indices: 100220803--100220860 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
100220793 GAAATACGAA
100220803 AAAAATTATTTTAAAAATTTTTATATACT
1 AAAAATTATTTTAAAAATTTTTATATACT
*
100220832 AAAAATTATTTTAAAATTTTTTATATACT
1 AAAAATTATTTTAAAAATTTTTATATACT
100220861 TTCAAAGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (29 bp):
AAAAATTATTTTAAAAATTTTTATATACT
Found at i:100231705 original size:21 final size:21
Alignment explanation
Indices: 100231681--100231747 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
100231671 TAGCTATCAT
100231681 ATTTTGGTAAGTTCGTATTAC
1 ATTTTGGTAAGTTCGTATTAC
* ** * *
100231702 A-TTTGTTACA-TTATTTATCAT
1 ATTTTGGTA-AGTT-CGTATTAC
100231723 ATTTTGGTAAGTTCGTATTAC
1 ATTTTGGTAAGTTCGTATTAC
100231744 ATTT
1 ATTT
100231748 GTTACATTAT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 8 0.25
21 16 0.50
22 8 0.25
ACGTcount: A:0.25, C:0.09, G:0.13, T:0.52
Consensus pattern (21 bp):
ATTTTGGTAAGTTCGTATTAC
Found at i:100231722 original size:42 final size:42
Alignment explanation
Indices: 100231675--100231761 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
100231665 TGTTGTTAGC
100231675 TATCATATTTTGGTAAGTTCGTATTACATTTGTTACATTATT
1 TATCATATTTTGGTAAGTTCGTATTACATTTGTTACATTATT
100231717 TATCATATTTTGGTAAGTTCGTATTACATTTGTTACATTATT
1 TATCATATTTTGGTAAGTTCGTATTACATTTGTTACATTATT
100231759 TAT
1 TAT
100231762 GTTTAACTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.53
Consensus pattern (42 bp):
TATCATATTTTGGTAAGTTCGTATTACATTTGTTACATTATT
Found at i:100231939 original size:16 final size:16
Alignment explanation
Indices: 100231918--100231949 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
100231908 CATTAGGGTG
100231918 TAGCAGGATTTGTGTC
1 TAGCAGGATTTGTGTC
100231934 TAGCAGGATTTGTGTC
1 TAGCAGGATTTGTGTC
100231950 AATGTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.31, T:0.38
Consensus pattern (16 bp):
TAGCAGGATTTGTGTC
Found at i:100233197 original size:30 final size:30
Alignment explanation
Indices: 100233163--100233219 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
100233153 GCCATATGGT
*
100233163 CGTGTGCCCCACACGGTCATGTGACACAGC
1 CGTGTGCCCCACACAGTCATGTGACACAGC
100233193 CGTGTGCCCCACACAGTCATGTGACAC
1 CGTGTGCCCCACACAGTCATGTGACAC
100233220 GACCGTATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.21, C:0.37, G:0.25, T:0.18
Consensus pattern (30 bp):
CGTGTGCCCCACACAGTCATGTGACACAGC
Found at i:100235715 original size:20 final size:20
Alignment explanation
Indices: 100235685--100235737 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
100235675 GGTAGTTTAC
100235685 TTCTATCTTGATTTTCATGAG
1 TTCT-TCTTGATTTTCATGAG
100235706 TTCTTCTTGATTTTCATGAG
1 TTCTTCTTGATTTTCATGAG
100235726 TTCTTCTTGATT
1 TTCTTCTTGATT
100235738 CTACCTTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 28 0.88
21 4 0.12
ACGTcount: A:0.15, C:0.15, G:0.13, T:0.57
Consensus pattern (20 bp):
TTCTTCTTGATTTTCATGAG
Found at i:100238252 original size:45 final size:43
Alignment explanation
Indices: 100238151--100238268 Score: 148
Period size: 45 Copynumber: 2.7 Consensus size: 43
100238141 CGGGCTTCGG
*
100238151 GCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGGCTTTGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGCCTTTGA
** * * *
100238194 GTTTAGTAAGCTATGATGCCGGTGAAAT-ATTATTCGAGCCTTTGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATGA-TA-TCG-GCCTTTGA
100238239 GCCTAGCAGGCTATAATGCCGGTGAAATGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATGA
100238269 AATGTTATGT
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
42 1 0.02
43 25 0.42
44 3 0.05
45 30 0.50
46 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (43 bp):
GCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGCCTTTGA
Found at i:100238599 original size:38 final size:38
Alignment explanation
Indices: 100238565--100238735 Score: 211
Period size: 38 Copynumber: 4.5 Consensus size: 38
100238555 GTAGGCTATA
*
100238565 TGCTGGAATTATATCCGAGTTAAATCCCGCAGGCTTCG
1 TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
* *
100238603 TGCTAGTAA-TATATCTGGGTTAAATCCCGCAGGCTTCG
1 TGCT-GGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
* *
100238641 TGCTGGTAA-TATATCCGGGTTAATTCCCACAGGCTTCG
1 TGCTGG-AATTATATCCGGGTTAAATCCCGCAGGCTTCG
* * * *
100238679 TGCTAGTATTATATCCGGGTTAAATCCCGCAGGCCTAG
1 TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
* *
100238717 TGCTGGTATTATATTCGGG
1 TGCTGGAATTATATCCGGG
100238736 CCTTTGAGCC
Statistics
Matches: 115, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
37 2 0.02
38 110 0.96
39 3 0.03
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.32
Consensus pattern (38 bp):
TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
Found at i:100238674 original size:76 final size:76
Alignment explanation
Indices: 100238565--100238735 Score: 245
Period size: 76 Copynumber: 2.2 Consensus size: 76
100238555 GTAGGCTATA
* * *
100238565 TGCTGG-AATTATATCCGAGTTAAATCCCGCAGGCTTCGTGCTAGTAATATATCTGGGTTAAATC
1 TGCTGGTAA-TATATCCGGGTTAAATCCCACAGGCTTCGTGCTAGTAATATATCCGGGTTAAATC
* *
100238629 CCGCAGGCTTCG
65 CCGCAGGCCTAG
* *
100238641 TGCTGGTAATATATCCGGGTTAATTCCCACAGGCTTCGTGCTAGTATTATATCCGGGTTAAATCC
1 TGCTGGTAATATATCCGGGTTAAATCCCACAGGCTTCGTGCTAGTAATATATCCGGGTTAAATCC
100238706 CGCAGGCCTAG
66 CGCAGGCCTAG
* *
100238717 TGCTGGTATTATATTCGGG
1 TGCTGGTAATATATCCGGG
100238736 CCTTTGAGCC
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
76 83 0.98
77 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.32
Consensus pattern (76 bp):
TGCTGGTAATATATCCGGGTTAAATCCCACAGGCTTCGTGCTAGTAATATATCCGGGTTAAATCC
CGCAGGCCTAG
Found at i:100238778 original size:45 final size:45
Alignment explanation
Indices: 100238728--100238857 Score: 199
Period size: 45 Copynumber: 2.9 Consensus size: 45
100238718 GCTGGTATTA
*
100238728 TATTCGGGCCTTTGAGCCTAGCAGGCTATTATGCCGATGAGACAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGATGAGACAC
* * *
100238773 TATTCGGGCCTTTGGGCCTAGCAGGCTATAATGCCGGTGAGATAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGATGAGACAC
*
100238818 TATTTGGG-CTTTCGAGCCTAGCAGGCTATAATGCCGATGA
1 TATTCGGGCCTTT-GAGCCTAGCAGGCTATAATGCCGATGA
100238858 AATGATAATC
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
44 4 0.05
45 73 0.95
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (45 bp):
TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGATGAGACAC
Found at i:100250677 original size:56 final size:57
Alignment explanation
Indices: 100250610--100250725 Score: 207
Period size: 56 Copynumber: 2.1 Consensus size: 57
100250600 AAATTGTAAT
* *
100250610 TTACCATAATAATAGTGAATATAATTTCTACTTATGATGTTTACAACTTATTTTA-A
1 TTACCATAATAATAGTGAATATAATTTCTAATTATGATGTTTACAACTCATTTTATA
100250666 TTACCATAATAATAGTGAATATAATTTCTAATTATGATGTTTACAACTCATTTTATA
1 TTACCATAATAATAGTGAATATAATTTCTAATTATGATGTTTACAACTCATTTTATA
100250723 TTA
1 TTA
100250726 AACCTTATTT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
56 53 0.93
57 4 0.07
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (57 bp):
TTACCATAATAATAGTGAATATAATTTCTAATTATGATGTTTACAACTCATTTTATA
Found at i:100251137 original size:20 final size:21
Alignment explanation
Indices: 100251085--100251138 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
100251075 TAACCTTATT
* * *
100251085 TTTCTATTTAATTTTTTTCTA
1 TTTCTATTTTATATCTTTCTA
*
100251106 TTT-TACTTTATATCTTT-TA
1 TTTCTATTTTATATCTTTCTA
100251125 TTTCTATTTTATAT
1 TTTCTATTTTATAT
100251139 AATTTATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 5 0.19
20 19 0.70
21 3 0.11
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTCTATTTTATATCTTTCTA
Found at i:100251148 original size:25 final size:24
Alignment explanation
Indices: 100251090--100251149 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 24
100251080 TTATTTTTCT
*
100251090 ATTTAATTTTTTTCTATTTTACTTT
1 ATTT-ATTTTTTTCTATTTTACTTA
* *
100251115 ATATCTTTTATTTCTATTTTA-TATA
1 ATTTATTTT-TTTCTATTTTACT-TA
100251140 ATTTATTTTT
1 ATTTATTTTT
100251150 ACATAATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
24 6 0.21
25 22 0.79
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (24 bp):
ATTTATTTTTTTCTATTTTACTTA
Found at i:100251155 original size:15 final size:15
Alignment explanation
Indices: 100251131--100251161 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
100251121 TTTATTTCTA
*
100251131 TTTTATATAATTTAT
1 TTTTACATAATTTAT
100251146 TTTTACATAATTTAT
1 TTTTACATAATTTAT
100251161 T
1 T
100251162 CTCAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTACATAATTTAT
Found at i:100252177 original size:27 final size:27
Alignment explanation
Indices: 100252147--100252201 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
100252137 TGGGTGAGAT
100252147 TGAATTCAGAAAGATTCAAGGAAGGCA
1 TGAATTCAGAAAGATTCAAGGAAGGCA
100252174 TGAATTCAGAAAGATTCAAGGAAGGCA
1 TGAATTCAGAAAGATTCAAGGAAGGCA
100252201 T
1 T
100252202 TTCCTGATCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.11, G:0.25, T:0.20
Consensus pattern (27 bp):
TGAATTCAGAAAGATTCAAGGAAGGCA
Found at i:100268487 original size:13 final size:13
Alignment explanation
Indices: 100268469--100268493 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
100268459 TCTTGGTTCA
100268469 CACGGCCGTGTCG
1 CACGGCCGTGTCG
100268482 CACGGCCGTGTC
1 CACGGCCGTGTC
100268494 TATCTTTGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.40, G:0.36, T:0.16
Consensus pattern (13 bp):
CACGGCCGTGTCG
Found at i:100275203 original size:31 final size:31
Alignment explanation
Indices: 100275160--100275233 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
100275150 TTAAAGAGTT
*
100275160 ACACGCCAGTGTAAATGGGCCGTGTGTACTC
1 ACACGCCCGTGTAAATGGGCCGTGTGTACTC
100275191 ACACGCCCGTGTAAATGGGCCGTGTGTACTC
1 ACACGCCCGTGTAAATGGGCCGTGTGTACTC
100275222 ACACGCCCGTGT
1 ACACGCCCGTGT
100275234 GACTTGGGAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.20, C:0.30, G:0.28, T:0.22
Consensus pattern (31 bp):
ACACGCCCGTGTAAATGGGCCGTGTGTACTC
Found at i:100284629 original size:54 final size:54
Alignment explanation
Indices: 100284567--100284671 Score: 174
Period size: 54 Copynumber: 1.9 Consensus size: 54
100284557 TCCTACACCG
*
100284567 ATGGGAAGGAACCTTGTGTCACACACGGTCTAAACACACGCCCGTGTGTCCGCC
1 ATGGGAAGGAACCGTGTGTCACACACGGTCTAAACACACGCCCGTGTGTCCGCC
** *
100284621 ATGGGAAGGATTCGTGTGTCACACACGGTCTAAACACACGCTCGTGTGTCC
1 ATGGGAAGGAACCGTGTGTCACACACGGTCTAAACACACGCCCGTGTGTCC
100284672 AACCATGTGG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.21
Consensus pattern (54 bp):
ATGGGAAGGAACCGTGTGTCACACACGGTCTAAACACACGCCCGTGTGTCCGCC
Found at i:100285275 original size:33 final size:33
Alignment explanation
Indices: 100285233--100285298 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
100285223 AAGCATTTAC
100285233 ATGCTTAGTAAGCTCGAATAACCGAAAAGTAAA
1 ATGCTTAGTAAGCTCGAATAACCGAAAAGTAAA
100285266 ATGCTTAGTAAGCTCGAATAACCGAAAAGTAAA
1 ATGCTTAGTAAGCTCGAATAACCGAAAAGTAAA
100285299 CTTACCGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.21
Consensus pattern (33 bp):
ATGCTTAGTAAGCTCGAATAACCGAAAAGTAAA
Found at i:100287955 original size:56 final size:56
Alignment explanation
Indices: 100287869--100287988 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
100287859 ACAAGGGATG
100287869 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
100287925 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
100287981 ATGGGCAA
1 ATGGGCAA
100287989 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:100289214 original size:40 final size:41
Alignment explanation
Indices: 100289118--100289222 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 41
100289108 CGAATGATGT
* *
100289118 CCGGGCTAAGTCCTGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCATAA
* * * *
100289158 CCGGACTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTATAA
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCTAAGTGACCATAA
*
100289198 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
100289223 AACGAGTAGC
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
39 1 0.02
40 45 0.83
41 8 0.15
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (41 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCATAA
Found at i:100302053 original size:47 final size:47
Alignment explanation
Indices: 100301992--100302339 Score: 570
Period size: 47 Copynumber: 7.4 Consensus size: 47
100301982 CAGCCAAGAC
*
100301992 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
100302039 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
100302086 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
100302133 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
** *
100302180 AGTGTATATGCGTGATAAGGCCTAATTGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
100302227 AGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * *
100302274 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
100302321 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
100302340 TCCCGAAGGG
Statistics
Matches: 281, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 281 1.00
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:100302514 original size:37 final size:37
Alignment explanation
Indices: 100302458--100302536 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
100302448 CCGAGCTCTA
* *
100302458 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
100302495 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
100302532 AAGAC
1 AAGAC
100302537 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:100308129 original size:12 final size:12
Alignment explanation
Indices: 100308103--100308137 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
100308093 AGCAAGAGTC
100308103 AAAAGGAGC-AA
1 AAAAGGAGCAAA
100308114 AAAAGGAGCAAA
1 AAAAGGAGCAAA
100308126 AAAAGGA-CAAA
1 AAAAGGAGCAAA
100308137 A
1 A
100308138 TGGACCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.69, C:0.09, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAAGGAGCAAA
Found at i:100308137 original size:21 final size:23
Alignment explanation
Indices: 100308103--100308146 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
100308093 AGCAAGAGTC
*
100308103 AAAAGGAGCAAAAAAGGAGCAAA
1 AAAAGGAGCAAAAAAGGACCAAA
*
100308126 AAAAGGA-C-AAAATGGACCAAA
1 AAAAGGAGCAAAAAAGGACCAAA
100308147 TCGAGAAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 1 0.05
23 7 0.37
ACGTcount: A:0.64, C:0.11, G:0.23, T:0.02
Consensus pattern (23 bp):
AAAAGGAGCAAAAAAGGACCAAA
Found at i:100313345 original size:40 final size:40
Alignment explanation
Indices: 100313308--100314213 Score: 1683
Period size: 40 Copynumber: 22.6 Consensus size: 40
100313298 GCTACTCGTT
* *
100313308 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
100313348 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
100313388 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
100313428 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
100313468 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
100313508 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
100313548 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
100313588 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
100313628 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
100313668 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
100313708 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
100313748 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
100313788 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
100313828 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
100313868 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
100313908 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
100313948 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
100313988 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
100314028 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
100314068 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
100314108 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
100314148 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
100314189 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
100314214 CATCATTCAA
Statistics
Matches: 853, Mismatches: 9, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
39 3 0.00
40 837 0.98
41 13 0.02
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:100318448 original size:5 final size:5
Alignment explanation
Indices: 100318438--100318503 Score: 82
Period size: 5 Copynumber: 12.8 Consensus size: 5
100318428 ATTCTTAATT
100318438 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTTTA TTTTCA TTTTCA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA --TTTTA TTTT-A TTTT-A
100318487 TTTTA --TTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTT
100318504 GAAAGACATA
Statistics
Matches: 56, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
3 3 0.05
5 37 0.66
6 11 0.20
7 5 0.09
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:100318473 original size:32 final size:34
Alignment explanation
Indices: 100318424--100318503 Score: 114
Period size: 32 Copynumber: 2.4 Consensus size: 34
100318414 CCTCCTAACT
100318424 TTTTATTCTTAATTTTTTATTTT-ATTTT-ATTTTA
1 TTTTATT-TT-ATTTTTTATTTTCATTTTCATTTTA
100318458 TTTTATTTTATTTTTTATTTTCATTTTCATTTTA
1 TTTTATTTTATTTTTTATTTTCATTTTCATTTTA
100318492 --TTATTTTATTTT
1 TTTTATTTTATTTT
100318504 GAAAGACATA
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
32 24 0.55
33 7 0.16
34 13 0.30
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.78
Consensus pattern (34 bp):
TTTTATTTTATTTTTTATTTTCATTTTCATTTTA
Found at i:100318478 original size:39 final size:37
Alignment explanation
Indices: 100318425--100318503 Score: 97
Period size: 39 Copynumber: 2.1 Consensus size: 37
100318415 CTCCTAACTT
*
100318425 TTTATTCTTAATTTTTTATTTT-ATTTTATTTTATTTTAT
1 TTTATTCTTAA-TTTTCATTTTCATTTTA--TTATTTTAT
* *
100318464 TTTATTTTTTATTTTCATTTTCATTTTATTATTTTAT
1 TTTATTCTTAATTTTCATTTTCATTTTATTATTTTAT
100318501 TTT
1 TTT
100318504 GAAAGACATA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 12 0.33
38 9 0.25
39 15 0.42
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (37 bp):
TTTATTCTTAATTTTCATTTTCATTTTATTATTTTAT
Found at i:100329886 original size:46 final size:46
Alignment explanation
Indices: 100329836--100329985 Score: 142
Period size: 46 Copynumber: 3.2 Consensus size: 46
100329826 CGTGTCACAC
* *
100329836 GTCTTACTCTAGCTCTCATAATGTGGCTGATGCATGTCCCAGACAT
1 GTCTTACACTAGCTCTCATAATGTGGCCGATGCATGTCCCAGACAT
* * * * * *
100329882 GTCTTACACTAGCCCTCGT-CTG-GATGCCGATTCCATGCCCCTGACAT
1 GTCTTACACTAGCTCTCATAATGTG--GCCGA-TGCATGTCCCAGACAT
* * * *
100329929 GGTCTTACACTGGCTCTAATAATGTGGCCGAAGCATGTCCCAAACAT
1 -GTCTTACACTAGCTCTCATAATGTGGCCGATGCATGTCCCAGACAT
100329976 GTCTTACACT
1 GTCTTACACT
100329986 GGCGCACAAA
Statistics
Matches: 80, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
44 1 0.01
45 2 0.03
46 30 0.38
47 24 0.30
48 20 0.25
49 2 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.29
Consensus pattern (46 bp):
GTCTTACACTAGCTCTCATAATGTGGCCGATGCATGTCCCAGACAT
Found at i:100333408 original size:49 final size:48
Alignment explanation
Indices: 100333334--100333503 Score: 161
Period size: 49 Copynumber: 3.6 Consensus size: 48
100333324 TTACAGCCAA
* * *
100333334 TGTAAGACCTCTCTAGGACACGGCATCGGCCTCAAGATATGCAAGCTAG
1 TGTAAGACCTATCTAGGACATGGCATCGGCCTCAAGATATG-AAGTTAG
* * * ** *
100333383 TGTAAGACCTATCTAGGAGATGGCATCAG-CT--TGAGGTG-TGTTAG
1 TGTAAGACCTATCTAGGACATGGCATCGGCCTCAAGATATGAAGTTAG
* * *
100333427 TATAAGACCTATCTGGGACATGGTATCGGCCTCAA-AGTATGTAAGTTAG
1 TGTAAGACCTATCTAGGACATGGCATCGGCCTCAAGA-TATG-AAGTTAG
*
100333476 TGTAAGACCTGTCTAGGACATGGCATCG
1 TGTAAGACCTATCTAGGACATGGCATCG
100333504 ACTTAGATGT
Statistics
Matches: 93, Mismatches: 22, Indels: 12
0.73 0.17 0.09
Matches are distributed among these distances:
44 28 0.30
45 2 0.02
46 5 0.05
47 2 0.02
48 2 0.02
49 54 0.58
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (48 bp):
TGTAAGACCTATCTAGGACATGGCATCGGCCTCAAGATATGAAGTTAG
Found at i:100334822 original size:21 final size:22
Alignment explanation
Indices: 100334782--100334823 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
100334772 GTCAAGAAAG
*
100334782 CCACACGGGCGTGTTGCCCCTC
1 CCACACGAGCGTGTTGCCCCTC
*
100334804 CCACACGAGTGTG-TGCCCCT
1 CCACACGAGCGTGTTGCCCCT
100334824 ATTTCAAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.12, C:0.43, G:0.26, T:0.19
Consensus pattern (22 bp):
CCACACGAGCGTGTTGCCCCTC
Found at i:100341708 original size:10 final size:12
Alignment explanation
Indices: 100341682--100341711 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
100341672 GCCACACAAC
100341682 GTGTGCTAGGTT
1 GTGTGCTAGGTT
100341694 GTGTGCTAGGTT
1 GTGTGCTAGGTT
100341706 GTGTGC
1 GTGTGC
100341712 CAGACTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.07, C:0.10, G:0.43, T:0.40
Consensus pattern (12 bp):
GTGTGCTAGGTT
Found at i:100342752 original size:26 final size:27
Alignment explanation
Indices: 100342699--100342752 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
100342689 TTAATAATTC
* *
100342699 TGGACTTTTGATTTTTAGGTAAATTTT
1 TGGACTTTTGATATTTAGGTAAAGTTT
* *
100342726 TGGA-TTTTGATATTTAGTTTAAGTTT
1 TGGACTTTTGATATTTAGGTAAAGTTT
100342752 T
1 T
100342753 CTGCATGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.22, C:0.02, G:0.19, T:0.57
Consensus pattern (27 bp):
TGGACTTTTGATATTTAGGTAAAGTTT
Done.